KLF3 mediates epidermal differentiation through the epigenomic writer CBP [ChIP-seq]

The differentiated layers of the epidermis protect the body from the outside environment. Impairments in the differentiation process can lead to skin diseases that can afflict ~20% of the population. Thus, it is of utmost importance to characterize and understand the factors that promote the differentiation process. Here we identify the transcription factor KLF3 as a novel regulator of epidermal differentiation. Knockdown of KLF3 results in reduced differentiation gene expression and increased cell cycle gene expression. Over 50% of KLF3's genomic binding sites occur at regions containing H3K4me/H3K27ac with the vast majority at active enhancers. KLF3 bound to active enhancers proximal to differentiation genes that are dependent upon KLF3 for expression. Based on this association, we sought to investigate KLF3's possible relationship with the enhancer associated proteins CBP and P300. Analysis of the transcriptome controlled by CBP and P300 showed that CBP and KLF3 control a similar gene expression program and are both essential for promoting differentiation. In addition, 35% of CBP's genomic binding sites overlap with KLF3 and knockdown of KLF3 results in reduced CBP localization at enhancers proximal to differentiation gene clusters. Our results suggest that KLF3 regulates differentiation gene expression by promoting CBP localization at enhancers. Overall design: KLF3 and CBP ChIP seq in day 3 differentated primary keratinocytes. KLF3 knockdown ChIP-seq using CBP antibody

表皮的分层结构可保护机体免受外界环境的侵害。分化过程出现异常可引发皮肤疾病，影响约20%的人群，因此对促进表皮分化的相关因子进行表征与机制解析具有极其重要的意义。本研究鉴定出转录因子KLF3为表皮分化的新型调控因子。敲低KLF3会导致分化相关基因的表达水平下调，同时使细胞周期相关基因的表达水平上调。超过50%的KLF3基因组结合位点位于带有H3K4me/H3K27ac修饰的染色质区域，且绝大多数结合位点分布于活性增强子区域。KLF3结合于依赖其表达的分化相关基因近端的活性增强子区域。基于这一结合关联，本研究进一步探究了KLF3与增强子相关蛋白CBP、P300之间的潜在相互作用关系。对CBP与P300调控的转录组进行分析后发现，CBP与KLF3调控的基因表达程序高度相似，且二者均为促进表皮分化所必需的因子。此外，CBP 35%的基因组结合位点与KLF3的结合位点存在重叠；且敲低KLF3会导致CBP在分化相关基因簇近端增强子区域的定位水平下降。本研究结果表明，KLF3通过促进CBP在增强子区域的定位，进而调控分化相关基因的表达。实验整体设计：在分化第3天的原代角质形成细胞中开展KLF3与CBP的染色质免疫共沉淀测序（ChIP-seq）实验；同时使用CBP抗体开展KLF3敲低后的ChIP-seq实验。